Tuesday, August 23, 2011

The Oldest Cells

I was going to write about the discovery of the oldest fossil cells but Jerry Coyne beat me to the punch [Newly found: the world’s oldest fossils!]. The new fossil bacteria are thought to be 3.4 billion years old and they were discovered in Australia only a few kilometers from the site where the so-called "cyanobacteria" fossils were discovered almost twenty years ago. Those fossils were reported to be even older (3.5 billion years) but the discovery has been completely discredited. The "fossils" aren't fossils [Did Life Arise 3.5 Billion Years Ago?]. That makes this discovery the oldest known cells (Wacey, 2011).

Interestingly, the senior author on this paper is Martin Brasier and he was one of the scientists who challenged the earlier result of William Schopf. Read all about it on Jerry Coyne's blog website.

The fossils are associated with a sulfur-rich mineral called pyrite. This mineral is produced by modern sulfate-reducing bacteria and it's reasonable to assume that the primitive bacteria detected in these ancient rocks also carried out sulfate reduction. That's not surprising since there wasn't much oxygen in the deep ocean 3.5 billion years ago.

Jerry Coyne didn't explain the biochemistry so let me give it a try. We need to start with a brief lesson on how modern living bacteria make ATP. The key to this understanding is a knowledge of Oxidation-Redution Reactions—one of the important basic concepts in biochemistry [see also Pushing Electrons].

Oxidation reactions are reactions where one or more electrons are given up. They are always coupled to reduction reactions that take up electrons. The direction of electron flow will depend on something called the "reduction potential" of the two half reactions. For our purposes we can think of the oxidation reaction as giving up "high energy" electrons that lose some of their energy before being taken up by the reduction reaction. It's this loss of energy that drives ATP synthesis.

Here's a simplified (!?) version of the electron transport pathway in the cell membranes of bacteria or mitochondria. The initial oxidation reaction is on the left below the membrane. NADH is a molecule produced during cell metabolism; notably glycolysis (degradation of glucose) and the citric acid cycle. NADH is the electron donor.

The electrons given up by NADH travel through various enzyme complexes that are embedded in the membrane (follow the red line). As the electrons give up some of their energy, the complexes pump protons from the inside of the cell to the outside. This sets up a proton gradient across the membrane and that gradient is used to drive ATP synthesis by ATP Synthase as the protons move back into the cell. This is the essence of chemiosmotic theory for which Peter Mitchell won the Nobel Prize in 1978. It's the most important pathway in all of biochemistry so every biochemist should know it intimately (they don't).

The electrons have to go somewhere eventually. The terminal electron acceptor in most modern species is molecular oxygen (O2) as shown in the figure. This is why we need oxygen to survive.

There are many modern species of bacteria that use different electron donors and electron acceptors to create the proton gradient. We're interested in those that use inorganic electron donors and something other than oxygen as an electron acceptor since those kind of bacteria are going to give us clues about the metabolism of primitive bacterial cells such as those preserved in the 3.4 billion year old rocks.

Here's a possible scheme based on what we know about modern sulfur-reducing bacteria.

The electron donor in this case is molecular hydrogen (H2). This avoids the need to use organic compounds such as NADH and glucose as a source of electrons. Hydrogen is just one of many possible electron donors but it happens to be one of the donors used by sulfur-reducing bacteria.

The electrons pass through various cytochrome complexes that are simplified versions of the ones in the first figure but they achieve the same purpose [Ubiquinone and the Proton Pump].

The electron acceptor is sulfate (SO42-). It is reduced (gaining electrons) to hydrogen sulfide (HS) which reacts with iron to produce the mineral pyrite. These bacteria do not need oxygen and they do not need an external source of energy in the form of a complex organic molecule.

We understand a lot about basic metabolism and bioenergetics and we can deduce the basic evolution of the modern complex pathways through studying unusual bacterial species that have adapted to unique environments, such as those that lack oxygen.

Sulfur-reducing (the bacteria described in the paper) and sulfate-reducing (which you describe here) are not the same thing. These bacteria were reducing elemental sulfur, arising from sulfogenic photosynthesis (which predated oxygenic photosynthesis by perhaps almost 1 billion years).

In the paper they talk about sulfate-reducing bacteria, not sulfur-reducing bacteria. So that's what I described.

Initially I thought they were describing a metabolism involving the oxidation of hydrogen sulfide and I thought it would be fun to describe a different electron donor in the electron transport chain.

There's no evidence that these bacteria were capable of photosynthesis so I don't think we are considering that at all. We certainly don't expect the earliest forms of life to be capable of photosynthesis.

What I find fascinating about the electron transport chain is how the mitochondrion makes use of the laws of physics to perform its function. That is a general principle we can see throughout the intelligent functioning of the cell.

"This sets up a proton gradient across the membrane and that gradient is used to drive ATP synthesis by ATP Synthase as the protons move back into the cell."

This is the heart of the process and the most striking use of the laws of physics by the mitochondrion. There must be many other uses of the laws of physics in the total process. Does anyone know of any articles or studies that analyzes cellular processes that way? I don't mean general descriptions of how processes occur but EXPLICITLY presenting how the steps make use of specific laws of physics. If so I would be very interested in seeing that material.

What I find fascinating about the electron transport chain is how the mitochondrion makes use of the laws of physics to perform its function.

Umm - what other laws would you like it to use?

Every single natural process and phenomenon in the universe "makes use of the laws of physics" to perform its function, from lightning strikes to stars shining to subatomic particles carrying forces and charges. Are they all intelligent, down to the subatomic particles?

What I find fascinating about the electron transport chain is how the mitochondrion makes use of the laws of physics to perform its function.

Blink. Life is all about chemistry and energy. ie, physics. And really, it's largely about electrons. Their donation, receipt and sharing between atoms stabilises molecules.

http://en.wikipedia.org/wiki/Ionic_bond

http://en.wikipedia.org/wiki/Covalent_bond

http://en.wikipedia.org/wiki/Hydrogen_bond

These electron-mediated bonds (mostly the latter 2) form the stuff of life. Covalent bonding gives a stable structure to the DNA and protein backbones; hydrogen bonding allows DNA bases to pair in strict purine-pyrimidine linkage. This is at the heart of both replication (preservation of genotype) and translation/transcription (expression of phenotype) - ie, 'making use of the laws of physics'.

Biological energetics is all about electrons. Steal them from water using the energy of the sun and you have a convertible energy source that you can store in a number of ways - in bonds, or as an electrochemical gradient that can turn the 'water wheel' that is the rotary ATPase, storing the energy in bonds. ATP is the stock energetic intermediate of the cell, and - no coincidence, and neatly circular - is the source of the informational "A" in the DNA base set A,T,C and G.

Allan Miller, does it strike you as very interesting how the different levels all work together? Each level exists on its own (with its own rules and dynamics) but also integrates seamlessly across the levels. We all take this for granted but it is quite striking when you start to really focus on it.

"Allan Miller, does it strike you as very interesting how the different levels all work together? Each level exists on its own (with its own rules and dynamics) but also integrates seamlessly across the levels. We all take this for granted but it is quite striking when you start to really focus on it."

Integrating across levels like that would be quite a challenge for human designers. If we ever tried itTo think that that integration just happened without intent or intelligence is quite a leap of faith. It is more plausible and credible to conclude that intelligence and intent underlies it all.

It is more plausible and credible to conclude that intelligence and intent underlies it all.

Not for me it ain't. I see complexity building up from blind integration of simpler subunits. There is certainly a hierarchy - Quarks, electrons, photons, energy and forces (thanks, Big Bang!) to protons and neutrons and atoms and the periodic table (cheers, Gravity!) to molecules to, in the right environment, replicators (good old Earth; good old Sun - thanks again, Gravity!) to phenotypically-assisted replication to cells to competitive/cooperative ecosystems to multicellular colonies to neural networks to intelligence (of a sort) to societies.

There is no logic or plausibility to me in starting with intelligence and intent. Complexity arises from simplicity, not from even greater antecedent complexity. I know this means a lot to you, but I just don't buy it.

The design we see in the areas we are discussing are the opposite of kludges. Anyone who knows design principles can see that. But that is so obvious to those who know about such things that it is pointless to argue with others who do not know about these things.

The design we see in the areas we are discussing are the opposite of kludges. Anyone who knows design principles can see that.But that is so obvious to those who know about such things that it is pointless to argue with others who do not know about these things.

Sorry Anon, but I think what I think; there is no point in getting snooty with me for my perspective. I work in software design and have a degree in molecular biology. So I think I'm reasonably placed to see the ways in which the genome does, and doesn't, adhere to principles of design.

DNA is a bit like a book, or a computer program, organisms are a bit like machines, and all those things need designers, ergo ... ? Ergo nothing. Viable genomes are much less tightly-specified than books or programs, and organisms resemble machines barely at all. And just because one set of phenomena has intentional design does not justify the inference that this is a requirement for all phenomena you choose to lump in with them.

You've got it the wrong way round. Intelligent Designers came on the scene with tool use and language. They create things that are a bit like the natural products of a designer-free world.

Your Designer bears no resemblance to human designers - it is not made of physical stuff, and yet can interact with physical stuff by mechanisms unknown. And this complex entity came into existence by mechanisms that required no designer, pulled up by its own bootstraps?

From a conviction that complexity and utility demand intent, ID solves a non-existent problem by the invention of an impossible entity, and scorns biology for not simply setting aside 160 years of data that confirms the current paradigm in spades.

@Allan MillerSorry.I reposted another Anonymous’ remark from Friday, September 02, 2011 4:05:00 PM on Saturday, September 03, 2011 5:16:00 PM and Saturday, September 03, 2011 5:17:00 PM. I do not know whether the Anonymous of Friday, September 02, 2011 4:05:00 PM and of Sunday, September 04, 2011 9:39:00 AM are the same Anonymous or not.

@Anonymous of Sunday, September 04, 2011 9:39:00 AM I did not attack you or your family, or send threatening messages to your home.I do not know whether anyone attacked you or your family, or send threatening messages to your home.I do not understand whatever basis you can have for saying I did so.Could you lay off the rampant paranoia? In several comments you’ve been recommended to take mental counseling. That would be an eminently sensible course of action for you to take.

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Principles of Biochemistry 5th edition

Disclaimer

Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

Superstition

Quotations

The old argument of design in nature, as given by Paley, which formerlyseemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.

Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.

The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.

Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.

The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.